Ligand profile

31N

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02784 — DNA topoisomerase 4 subunit A

Via homolog PDB 4plb UniProt P20831 Formula C₂₆H₂₈FN₅O₅
Mol. weight 509.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
31N
PDB
4plb
UniProt (similar protein)
P20831
Target protein
KP13_02784

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 509.54 Da
LogP (Crippen) 2.28
H-bond donors 3
H-bond acceptors 9
TPSA 127.72 Ų
Rotatable bonds 7
Aromatic rings 3 / 7
Heavy atoms 37
Fraction sp³ C 0.46
Formula C₂₆H₂₈FN₅O₅

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 127.7
  • −1 ≤ LogP ≤ 5 2.28
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 509.5
  • LogP ≤ 5 2.28
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 127.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c(n1)c(c(cn2)F)C[C@@H](C34CCC(CC3)(CO4)NCc5ccc6c(n5)NC(=O)CO6)O
InChI 
InChI=1S/C26H28FN5O5/c1-35-22-5-3-18-23(32-22)16(17(27)12-28-18)10-20(33)26-8-6-25(7-9-26,14-37-26)29-11-15-2-4-19-24(30-15)31-21(34)13-36-19/h2-5,12,20,29,33H,6-11,13-14H2,1H3,(H,30,31,34)/t20-,25?,26?/m0/s1
InChIKey 
JWCUKLIKGBNEKA-WOEOTAOXSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00521

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02784.

PDB 22

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 15

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)